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comparison qiime2/qiime_diversity_beta-correlation.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 914fa4daf16a
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
22 22
23 #if str($pmethod) != 'None': 23 #if str($pmethod) != 'None':
24 --p-method=$pmethod 24 --p-method=$pmethod
25 #end if 25 #end if
26 26
27 #if $ppermutations: 27 #if str($ppermutations):
28 --p-permutations=$ppermutations 28 --p-permutations=$ppermutations
29 #end if 29 #end if
30 30
31 #if $pintersectids: 31 #if str($pintersectids):
32 --p-intersect-ids 32 --p-intersect-ids
33 #end if 33 #end if
34 34
35 35
36 36
55 --p-label2="$plabel2" 55 --p-label2="$plabel2"
56 #end if 56 #end if
57 57
58 58
59 59
60 #if $input_files_mmetadatafile: 60 #if $metadatafile:
61 #def list_dict_to_string(list_dict): 61 --m-metadata-file=$metadatafile
62 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
63 #for d in list_dict[1:]:
64 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
65 #end for
66 #return $file_list
67 #end def
68 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
69 #end if 62 #end if
63
64
65
70 66
71 --o-metadata-distance-matrix=ometadatadistancematrix 67 --o-metadata-distance-matrix=ometadatadistancematrix
72 --o-mantel-scatter-visualization=omantelscattervisualization 68 --o-mantel-scatter-visualization=omantelscattervisualization
73 ; 69 ;
74 cp ometadatadistancematrix.qza $ometadatadistancematrix; 70 cp ometadatadistancematrix.qza $ometadatadistancematrix;
86 </param> 82 </param>
87 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/> 83 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
88 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/> 84 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/>
89 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: 'Metadata']" name="plabel1" optional="True" type="text" value="Metadata"/> 85 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: 'Metadata']" name="plabel1" optional="True" type="text" value="Metadata"/>
90 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="Distance Matrix"/> 86 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="Distance Matrix"/>
91 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 87
92 <param label="--m-metadata-file" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 88 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="True" />
93 </repeat> 89
94 </inputs> 90 </inputs>
95 <outputs> 91 <outputs>
96 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/> 92 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/>
97 <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.qzv" name="omantelscattervisualization"/> 93 <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.qzv" name="omantelscattervisualization"/>
98 </outputs> 94 </outputs>